If the carpet is just worn out vs stained, dirty or gross then I wouldn't have an issue replacing it.

Replace damaged Exterior wood $1,00 , Plumbing/water supply NOT functional $400 ,  Paint/stain Exterior AS NEEDED  $300,  Repair Damaged Ceiling/Walls $400, Replace missing Flooring  $2,000 , Replace Hot Water Heater $800,  10% cushion $490 .....

Carpets are a little stained - woods under are decent ...

Morris is a stain on the entire real estate industry.

I would recommend not providing white towels for your guests due to make up stains.

All the ceiling were great with no leaks or stains. 

I did it in another nearby building and it's still decent 7 years later but for one stain from a leaking garbage bag, but this neighborhood is lower down the gentrification ladder.

When they move out in six months, they can't blame the stained carpet on the tenant that left.

I think for the carpet she has a legitimate reason to take your 1400 though over 5 years you might argue it should be replaced regardless of whether there are pet stains due to ordinary wear and tear.  

I suggested a MIXTURE of vinegar and water to clean,  when she complained that it has " mold" looking stain in the shower head.